ncbi-genome-download
eggnog-mapper
| ncbi-genome-download | eggnog-mapper | |
|---|---|---|
| 4 | 1 | |
| 893 | 536 | |
| - | 3.5% | |
| 5.7 | 4.3 | |
| 10 months ago | 2 months ago | |
| Python | Python | |
| Apache License 2.0 | GNU Affero General Public License v3.0 |
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ncbi-genome-download
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I have a question about the FTP of annotation files from NCBI's Genbank and RefSeq
If you have the taxonomic IDs of your organisms of interest, there are existing parallelized download tools that are more efficient like https://github.com/kblin/ncbi-genome-download or bit-dl-ncbi-assemblies from https://github.com/AstrobioMike/bit
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Bioinformatics without a lab
Downloading from NCBI can be pretty wonky though, but third parties have made good programs to deal with. As an example - and a personal favorite - you have https://github.com/kblin/ncbi-genome-download which by far is the easiest way to download various assembled genomes.
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Downloading genomes from database via command line FTP
I know you said Ensembl, but if you can live with NCBI, I would suggest https://github.com/kblin/ncbi-genome-download
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Downloading viral genomes programmatically
Useful tool to download from NCBI: ncbi-genome-download
eggnog-mapper
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Hail - Cloud-native genomic dataframes and batch computing
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